NEpy LIBRARY DEMO: $batch$
Main author: R Sanchez-Todo
Contributors: (are welcomed)Neuroelectrics Corporation
Created November 2018
Modified: -
CONTENTS
- Description
- Set up
- Get help
- Preprocess a directory
NOTE: Make sure you have gone through NEpy demo 1-Frida before starting with this one, it will help!
1. Description
`batch` is a funciton which you input a directory and it performs a Frida test for each of the files available. Such files have to be in any of these formats: `.easy`, `.easy.gz`, `.nedf` with a corresponding `.info` file if available. For each of the files, `batch` performs the following: ``` f = Frida(filepath, author=author, parameters=parameters) f.plotEEG() f.plotPSD() f.QC() f.preprocess(pipeline) f.QC() f.plotEEG() f.plotPSD() ```2. Set up
When runnign the next cell, three input boxes are going to appear asking for the necessary data to set up:
Your name or ID. Example:
R. Sanchez-TodoThe path where you have stored the NEpy repository. Copy paste the path into that box. Example:
C:\Users\roser.sanchez\Documents\Git\NEpy_v0.1.The path where you have stored the file(s) you want to process with batch (
.easy,.easy.gz,.info). Example:C:\Users\roser.sanchez\Documents\Git\NEpy_v0.1\sampledata
author = input('\033[1mUser name:\033[0m \n')
nepypath = input('\033[1mNEpy repository path:\033[0m \n ')
datapath = input('\033[1mData path:\033[0m \n ')
import sys
import os
import time
sys.path.append(nepypath)
from nepy.frida.frida import Frida
from nepy.frida.batch import processDirectory
print('\n')
%load_ext autoreload
%autoreload 2
print("______________________________________________")
print ("\nNotebook started:", time.strftime("%Y-%m-%d %H:%M"))
print("\nData located in this folder:",'\033[93m', datapath, '\033[0m')
os.listdir(datapath)
3. Get help
Don't know how to deal with batch? No worries, ask for help!
The help function (similar to MATLAB) will print a description and an exaple of use of the batch function.
help(processDirectory)
4. Preprocess a directory
It is really simple! You just need to copy the following line:
[processed, skipped] = processDirectory(datapath)The arguments pipeline and parameters (see help(Frida)) are optional.
parameters = {
'time_span': 60,
'grab_seconds': 10.,
'detrend_time': 10.,
'QCthreshold': 75.,
'QCmax': 30.,
'fline': 60.,
'Q': 30.,
'fL': 2.,
'fH': 45.,
'order': 5,
'reference_electrodes': ['Cz'],
'offset_limit': 1.,
'std_limit': 15.
}
[processed, skipped] = processDirectory(datapath, parameters=parameters)
END OF $batch$ DEMO